SpringSaLaD-Python-Viz/R_L_test.txt at master · Hlpred/SpringSaLaD-Python-Viz · GitHub

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*** TIME INFORMATION ***
Total time: 1.00E-2
dt: 1.00E-8
dt_spring: 1.00E-9
dt_data: 1.00E-4
dt_image: 1.00E-4

*** SYSTEM INFORMATION ***
L_x: 0.1
L_y: 0.1
L_z_out: 0.01
L_z_in: 0.09
Partition Nx: 10
Partition Ny: 10
Partition Nz: 10

*** MOLECULES ***

MOLECULE: "R" Membrane Number 5 Site_Types 3 Total_Sites 4 Total_Links 4 is2D false
{
     TYPE: Name "R" Radius 2.00000 D 1.000 Color RED STATES "State0"
     TYPE: Name "L" Radius 1.00000 D 1.000 Color ORANGE STATES "State0"
     TYPE: Name "Anchor" Radius 1.00000 D 2.000 Color GRAY STATES "Anchor"

     SITE 0 : Intracellular : Initial State 'State0'
          TYPE: Name "R" Radius 2.00000 D 1.000 Color RED STATES "State0"
          x 0.00000 y 11.23333 z 44.15556
     SITE 1 : Membrane : Initial State 'Anchor'
          TYPE: Name "Anchor" Radius 1.00000 D 2.000 Color GRAY STATES "Anchor"
          x 0.00000 y 14.70000 z 31.00000
     SITE 2 : Intracellular : Initial State 'State0'
          TYPE: Name "R" Radius 2.00000 D 1.000 Color RED STATES "State0"
          x 0.00000 y 18.41111 z 43.90556
     SITE 3 : Intracellular : Initial State 'State0'
          TYPE: Name "L" Radius 1.00000 D 1.000 Color ORANGE STATES "State0"
          x 0.00000 y 14.89444 z 36.11667

     LINK: Site 2 ::: Site 0
     LINK: Site 3 ::: Site 1
     LINK: Site 3 ::: Site 0
     LINK: Site 3 ::: Site 2

     Initial_Positions: Random
}

MOLECULE: "Adapter" Intracellular Number 5 Site_Types 2 Total_Sites 3 Total_Links 2 is2D false
{
     TYPE: Name "A" Radius 3.00000 D 1.000 Color BLUE STATES "State0"
     TYPE: Name "L" Radius 1.00000 D 1.000 Color GOLD STATES "State0"

     SITE 0 : Intracellular : Initial State 'State0'
          TYPE: Name "A" Radius 3.00000 D 1.000 Color BLUE STATES "State0"
          x 0.00000 y 23.13333 z 49.45000
     SITE 1 : Intracellular : Initial State 'State0'
          TYPE: Name "L" Radius 1.00000 D 1.000 Color GOLD STATES "State0"
          x 0.00000 y 22.88889 z 43.77778
     SITE 2 : Intracellular : Initial State 'State0'
          TYPE: Name "A" Radius 3.00000 D 1.000 Color BLUE STATES "State0"
          x 0.00000 y 22.42778 z 37.08333

     LINK: Site 0 ::: Site 1
     LINK: Site 1 ::: Site 2

     Initial_Positions: Random
}

*** MOLECULE FILES ***

MOLECULE: R null
MOLECULE: Adapter null

*** CREATION/DECAY REACTIONS ***

'R' : kcreate 0.0 kdecay 0.0
'Adapter' : kcreate 0.0 kdecay 0.0

*** STATE TRANSITION REACTIONS ***


*** ALLOSTERIC REACTIONS ***


*** BIMOLECULAR BINDING REACTIONS ***

'BindingReaction0'       'R' : 'R' : 'Any_State'  +  'Adapter' : 'A' : 'Any_State'  kon 10.0  koff 10.0  Bond_Length 1.0

*** MOLECULE COUNTERS ***

'R' : Measure Total Free Bound
'Adapter' : Measure Total Free Bound

*** STATE COUNTERS ***

'R' : 'R' : 'State0' : Measure Total Free Bound
'R' : 'L' : 'State0' : Measure Total Free Bound
'R' : 'Anchor' : 'Anchor' : Measure Total Free Bound
'Adapter' : 'A' : 'State0' : Measure Total Free Bound
'Adapter' : 'L' : 'State0' : Measure Total Free Bound

*** BOND COUNTERS ***

'BindingReaction0' : Counted

*** SITE PROPERTY COUNTERS ***

'R' Site 0 :  Track Properties true
'R' Site 1 :  Track Properties true
'R' Site 2 :  Track Properties true
'R' Site 3 :  Track Properties true
'Adapter' Site 0 :  Track Properties true
'Adapter' Site 1 :  Track Properties true
'Adapter' Site 2 :  Track Properties true

*** CLUSTER COUNTERS ***

Track_Clusters: true

*** SYSTEM ANNOTATIONS ***


*** MOLECULE ANNOTATIONS ***

Annotation: 'R'
{
}

Annotation: 'Adapter'
{
}

*** REACTION ANNOTATIONS ***

Annotation: 'BindingReaction0'
{
}